What this post suggests to me is that publishers need to change from a "book" model of selling their products to a "software" model. Software publishers today manage to sell products very like ebooks, with the same problems of "need to be quality-checked on every platform they run on" and "retailers want to use margin to gain share," yet they seem to be doing very well. The key is that many different strategies have been successful (for different products in different markets at different times) -- publishers will have to become as nimble in selling ebooks as software publishers have been forced to become in selling software. And, as with software, the pricing will be all over the map -- bestselling fiction for $4.99, technical titles for $499 -- as publishers learn what the market will bear. The transition to this model will occur as it did when video tapes moved from a "priced for rental" model to a "priced for sale" model in the 1980s -- same product + different market = entirely different price points.
The branding problem is an interesting one, and differs from the software model. On my computer, the user experience of the Apple-branded word processor, the Microsoft-branded word processor, and the several other brands of word processor differs enormously, but the content (the words they process and the things you can do to those words) is quite similar. But on my ebook reader, the user experience of the Tor-branded, Del Rey-branded, and DAW-branded ebooks is nearly identical although the content of each book is unique. This makes it tough for a brand to establish itself.
Some publishers will try to impose a "house look-and-feel" on their ebooks to create a brand. This won't work because the ebook experience is so malleable -- devices vary in their capabilities, and users want to impose their reading preferences (e.g. font and font size) which is one of the main selling points of the ebook over the paper book -- and anything the publisher does to put anything other than plain, readable text on the screen will be resisted by readers.
One thing that publishers can do to establish a brand is to make sure to nail the aspects that make one ebook better than another on the same platform. Make sure the illustrations are the best possible for the platform, make sure the table of contents works, enable any optional features, and do the right thing for every supported platform. This is a heck of a lot of work, but quality control in a multi-platform environment always is, and in the software business we have a saying that "quality doesn't cost money... quality makes money."
I think, though, that the bottom line for branding ebooks is identical to that for paper books. A publisher can get some aspects of a paper book right or wrong (font and font size, paper quality, binding) but fundamentally most paper books are quite similar -- ultimately the thing that readers will remember about a publisher, if they remember anything at all, is whether or not they consistently provide the kind of books they want to read. That's how to create a brand.